I just replaced my motherboard with the ASUS. It is working great! I did have to purchase a different CPU fan as the ASUS requires a 4 pin plug instead of the standard 3 pin. You can still use a 3 pin, but the fan runs at full RPM (~3650 RPM) and it is VERY loud. I replaced it with a Rocketfish 11D03A (Universal CPU Fan and Heatsink) and it is back to normal as far as sound.
Now, regarding the connectors. You can plug in the front panel audio to the motherboard. There is a direct plug for that connector. Next, you can plug in the USB panel to the motherboard as well. Those are direct. Now, there is a 5 pin (actually 4 pin) connector for the card reader. I plugged that into the bottom 4 pin connector on another USB interface on the motherboard and it's working without issue.
The biggest issue was the black connector that you showed above. I had to remove the wires from the connector. (very simple, just hold the lock up and pull the wire right out).
Then, I looked at the motherboard manual for the ASUS and plugged in each cable individually.
The breakdown is as follows:
Red/Red = Power Button
Green/Blue = Power LED
White/Yellow = HDD LED
Now I had to play with the LED wires as the
+/- are not marked. You'll know if they are reversed because the lights either won't work or they will not work as designed. It was a quick fix and now my computer is completely back to normal.